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Abstract
Eleven strains of methanogenic bacteria were divided into two groups on the basis of the directionality (oxidative or reductive) of their citric acid pathways. These pathways were readily identified for most methanogens from the patterns of carbon atom labeling in glutamate, following growth in the presence of [2-C]acetate. All used noncyclic pathways, but members of the family Methanosarcinaceae were the only methanogens found to use the oxidative direction. Methanococcus jannaschii failed to incorporate carbon from acetate despite transmembrane equilibration comparable to other weak acids. This organism was devoid of detectable activities of the acetate-incorporating enzymes acetyl coenzyme A synthetase, acetate kinase, and phosphotransacetylase. However, incorporation of [1-C]-, [2-C]-, or [3-C]pyruvate during the growth of M. jannaschii was possible and resulted in labeling patterns indicative of a noncyclic citric acid pathway operating in the reductive direction to synthesize amino acids. Carbohydrates were labeled consistent with glucogenesis from pyruvate. Leucine, isoleucine, phenylalanine, lysine, formate, glycerol, and mevalonate were incorporated when supplied to the growth medium. Lysine was preferentially incorporated into the lipid fraction, suggesting a role as a phytanyl chain precursor.
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Affiliation(s)
- G D Sprott
- Institute for Biological Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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2
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3
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Tonge PJ, Carey PR, Callender R, Deng H, Ekiel I, Muhandiram DR. Characterization of trans- and cis-5-methylthienylacryloyl chymotrypsin using Raman difference spectroscopy, NMR, and kinetics: carbonyl environment and reactivity. J Am Chem Soc 2002. [DOI: 10.1021/ja00072a031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Kozlov G, Trempe JF, Khaleghpour K, Kahvejian A, Ekiel I, Gehring K. Structure and function of the C-terminal PABC domain of human poly(A)-binding protein. Proc Natl Acad Sci U S A 2001; 98:4409-13. [PMID: 11287632 PMCID: PMC31848 DOI: 10.1073/pnas.071024998] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have determined the solution structure of the C-terminal quarter of human poly(A)-binding protein (hPABP). The protein fragment contains a protein domain, PABC [for poly(A)-binding protein C-terminal domain], which is also found associated with the HECT family of ubiquitin ligases. By using peptides derived from PABP interacting protein (Paip) 1, Paip2, and eRF3, we show that PABC functions as a peptide binding domain. We use chemical shift perturbation analysis to identify the peptide binding site in PABC and the major elements involved in peptide recognition. From comparative sequence analysis of PABC-binding peptides, we formulate a preliminary PABC consensus sequence and identify human ataxin-2, the protein responsible for type 2 spinocerebellar ataxia (SCA2), as a potential PABC ligand.
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Affiliation(s)
- G Kozlov
- Department of Biochemistry, McGill University and Montreal Joint Center for Structural Biology, 3655 Promenade Sir William Osler, Montreal, QC, Canada H3G 1Y6
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5
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Christendat D, Yee A, Dharamsi A, Kluger Y, Savchenko A, Cort JR, Booth V, Mackereth CD, Saridakis V, Ekiel I, Kozlov G, Maxwell KL, Wu N, McIntosh LP, Gehring K, Kennedy MA, Davidson AR, Pai EF, Gerstein M, Edwards AM, Arrowsmith CH. Structural proteomics of an archaeon. Nat Struct Biol 2000; 7:903-9. [PMID: 11017201 DOI: 10.1038/82823] [Citation(s) in RCA: 236] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A set of 424 nonmembrane proteins from Methanobacterium thermoautotrophicum were cloned, expressed and purified for structural studies. Of these, approximately 20% were found to be suitable candidates for X-ray crystallographic or NMR spectroscopic analysis without further optimization of conditions, providing an estimate of the number of the most accessible structural targets in the proteome. A retrospective analysis of the experimental behavior of these proteins suggested some simple relations between sequence and solubility, implying that data bases of protein properties will be useful in optimizing high throughput strategies. Of the first 10 structures determined, several provided clues to biochemical functions that were not detectable from sequence analysis, and in many cases these putative functions could be readily confirmed by biochemical methods. This demonstrates that structural proteomics is feasible and can play a central role in functional genomics.
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Affiliation(s)
- D Christendat
- Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto 610 University Ave, Toronto, Ontario, Canada M5G 2M9
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6
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Beglova N, Maliartchouk S, Ekiel I, Zaccaro MC, Saragovi HU, Gehring K. Design and solution structure of functional peptide mimetics of nerve growth factor. J Med Chem 2000; 43:3530-40. [PMID: 11000007 DOI: 10.1021/jm990441x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The C-D loop in nerve growth factor (NGF) is involved in binding to the NGF receptor, TrkA. It is flexible and adopts several different types conformations in different NGF crystal forms. We have previously shown that a small cyclic peptide derived from the C-D loop of NGF binds to the TrkA receptor by mimicking the structure of this loop. To understand structure-function relationships in NGF C-D loop mimetics, we have produced a series of peptides predicted to form different types of beta-turns. The peptides were tested for their ability to promote cell survival in serum-free medium and to induce TrkA tyrosine phosphorylation. NMR structural studies were used to determined the backbone conformation and the spatial orientation of side chains involved in binding to the TrkA receptor. Peptides that form type I or type gammaL-alphaR beta-turns were the most active. The variety of active loop conformations suggests that the mimetics (and NGF) accommodate the binding site on TrkA by an 'induced fit' mechanism. In agreement with this hypothesis, NMR relaxation measurements detected both fast and slow motion in the peptides. We also characterized a retro-inverso peptide derived from the NGF C-D loop. This D-amino acid cyclic peptide did not adopt a conformation homologous to the NGF C-D loop and was inactive. This may be representative of difficulties in producing structural and functional mimetics by retro-inverso schemes.
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Affiliation(s)
- N Beglova
- Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, 3655 Promenade Sir William Osler, Montréal, Québec H3G 1Y6, Canada
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7
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Kozlov G, Ekiel I, Beglova N, Yee A, Dharamsi A, Engel A, Siddiqui N, Nong A, Gehring K. Rapid fold and structure determination of the archaeal translation elongation factor 1beta from Methanobacterium thermoautotrophicum. J Biomol NMR 2000; 17:187-194. [PMID: 10959626 DOI: 10.1023/a:1008363304977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The tertiary fold of the elongation factor, aEF-1beta, from Methanobacterium thermoautotrophicum was determined in a high-throughput fashion using a minimal set of NMR experiments. NMR secondary structure prediction, deuterium exchange experiments and the analysis of chemical shift perturbations were combined to identify the protein fold as an alpha-beta sandwich typical of many RNA binding proteins including EF-G. Following resolution of the tertiary fold, a high resolution structure of aEF-1beta was determined using heteronuclear and homonuclear NMR experiments and a semi-automated NOESY assignment strategy. Analysis of the aEF-1beta structure revealed close similarity to its human analogue, eEF-1beta. In agreement with studies on EF-Ts and human EF-1beta, a functional mechanism for nucleotide exchange is proposed wherein Phe46 on an exposed loop acts as a lever to eject GDP from the associated elongation factor G-protein, aEF-1alpha. aEF-1beta was also found to bind calcium in the groove between helix alpha2 and strand beta4. This novel feature was not observed previously and may serve a structural function related to protein stability or may play a functional role in archaeal protein translation.
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Affiliation(s)
- G Kozlov
- McGill University, Department of Biochemistry, Montreal, PQ, Canada
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8
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Kozlov G, Gehring K, Ekiel I. Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor. Biochemistry 2000; 39:2572-80. [PMID: 10704206 DOI: 10.1021/bi991913c] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The solution structure of the second PDZ domain (PDZ2) from human phosphatase hPTP1E has been determined using 2D and 3D heteronuclear NMR experiments. The binding of peptides derived from the C-terminus of the Fas receptor to PDZ2 was studied via changes in backbone peptide and protein resonances. The structure is based on a total of 1387 nonredundant experimental NMR restraints including 1261 interproton distance restraints, 45 backbone hydrogen bonds, and 81 torsion angle restraints. Analysis of 30 lowest-energy structures resulted in rmsd values of 0.41 +/- 0.09 A for backbone atoms (N, Calpha, C') and 1.08 +/- 0.10 A for all heavy atoms, excluding the disordered N- and C-termini. The hPTP1E PDZ2 structure is similar to known PDZ domain structures but contains two unique structural features. In the peptide binding domain, the first glycine of the GLGF motif is replaced by a serine. This serine appears to replace a bound water observed in PDZ crystal structures that hydrogen bonds to the bound peptide's C-terminus. The hPTP1E PDZ2 structure also contains an unusually large loop following strand beta2 and proximal to the peptide binding site. This well-ordered loop folds back against the PDZ domain and contains several residues that undergo large amide chemical shift changes upon peptide binding. Direct observation of peptide resonances demonstrates that as many as six Fas peptide residues interact with the PDZ2 domain.
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Affiliation(s)
- G Kozlov
- NMR Group, Pharmaceutical Biotechnology Sector and Montreal Joint Center for Structural Biology, Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
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9
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Ekiel I, Banville D, Shen SH, Gehring K. Effect of peptide binding on amide proton exchange rates in the PDZ2 domain from human phosphatase hPTP1E. Biochem Cell Biol 1999; 76:334-40. [PMID: 9923702 DOI: 10.1139/bcb-76-2-3-334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Amide hydrogen-deuterium exchange rates were measured in the PDZ2 domain from human phosphatase hPTPIE by 1H-15N heteronuclear NMR spectroscopy. Protection factors were calculated for the slowly exchanging hydrogens in both the free PDZ2 domain and its complex with an octapeptide peptide, R-N-E-I-Q-S-L-V, derived from the C-terminus of the Fas receptor. Aside from a short alpha-helical region alpha1 (amino acids A-45 to D-49), the pattern of highly protected amides correlated well with the presence of hydrogen bonds in elements of the secondary structure. Hydrogen-bonded amides showed relatively fast exchange rates with half-lives of less than 9 h at pD 7.6 and 8 degrees C. Protection factors, calculated as the ratio of theoretical (denatured) and observed exchange rates, showed less dispersion in maximal values than did the actual exchange rates. This behavior and the large pH dependence of the exchange rates suggest that amide exchange is close to the EX2 limit. In this limit, exchange of the most protected amides occurs through a global unfolding mechanism. The free energy of the unfolding calculated from the largest protection factors is 4.8 +/- 0.4 kcal/mol (1 cal = 4.184 J). This deltaG(o) closely matches the value measured by experiments with guanidine hydrochloride and fluorescence emission spectroscopy. Peptide binding to PDZ2 resulted in mostly global effects and stabilized the folded domain by 1.4 kcal/mol.
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Affiliation(s)
- I Ekiel
- Pharmaceutical Biotechnology Sector, Biotechnology Research Institute, National Research Council of Canada, Montréal, QC.
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10
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Abstract
Fusion proteins are frequently used in the functional characterization of newly discovered proteins and to identify interacting partners. In our study of hPTP1E, a cytosolic protein tyrosine phosphatase, we used glutathione S-transferase (GST)-fusion protein of the second PDZ domain to identify interacting peptide motifs by peptide phage display. A consensus motif G X X V W L G was identified and found to be specific for binding to GST-PDZ2 as determined by ELISA, peptide displacement and by protein overlay. However, using nuclear magnetic resonance (NMR), no interaction of the peptide was observed with PDZ2 alone. In co-precipitation experiments using the consensus peptide cross-linked to Affi-Gel, only GST-PDZ2 (but not PDZ2 or GST alone) could be precipitated. These data suggest that there is a potential for identification of artifacts when using fusion proteins in peptide phage display, and one should exercise caution in interpreting these results. It is critical that the interaction be verified using a second, independent system.
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Affiliation(s)
- K K Murthy
- Biotechnology Research Institute, National Research Council Canada, Montreal, QC, Canada
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11
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Abstract
In hereditary cystatin C amyloid angiopathy (HCCAA), presence of the Leu68 --> Gln substitution in cystatin C is coupled to a decreased concentration of this major cysteine proteinase inhibitor in cerebrospinal fluid and leads to its amyloid deposition in the brain. We established a high-yield expression system for L68Q cystatin C in Escherichia coli resulting in inclusion body accumulation at a level of 40% of the total cellular protein. Refolding of protein from purified inclusion bodies yielded a pure, almost completely monomeric and active inhibitor. CD and NMR spectroscopy demonstrated that so produced L68Q cystatin C is folded, conformationally homogeneous, and structurally very similar to wild-type cystatin C. Incubation at pH 7.0-5.5 caused the cystatin C variant to dimerize rapidly. The molecular form present at pH 6.0 displayed a slightly increased amount of hydrophobic parts on the surface as measured by 1-anilinonaphthalene-8-sulfonic acid (ANS) binding. NMR results showed that the dimer has a structure similar to that of the wild-type cystatin C dimer formed as a result of slight denaturation. Under more acidic conditions, at pH 4.5, another stable unfolding intermediate of L68Q cystatin C was identified. This molecular form exists in a monomeric state, is characterized by changes in secondary structure according to far UV CD spectroscopy, and shows an altered ANS binding resembling that of a molten globule state. The acidic pH also caused an almost complete monomerization of preformed dimers. The state of denaturation of L68Q cystatin C in vivo is thus a critical factor for the concentration of active cysteine proteinase inhibitor in cerebrospinal fluid and likely also for the development of amyloidosis, in HCCAA patients.
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Affiliation(s)
- B Gerhartz
- Department of Clinical Chemistry, Institute of Laboratory Medicine, University of Lund, University Hospital, Sweden
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12
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Abstract
We present three experiments which serve to identify carbon and proton sidechain resonances in 13C-labeled proteins. The first is an improvement on the previously published H(C)CH-COSY experiment and comprises the application of gradients for coherence selection and a reduction in the phase cycle. The second experiment is a new (H)CCH-COSY with two carbon dimensions. The (H)CCH-COSY presents several advantages over the H(C)CH-COSY experiment in terms of better sensitivity, improved resolution and easier identification of amino acid spins systems. The third experiment is a 2D proton-edited (H)C(C)H-COSY that allows suppression of methylene resonances. All three HCCH-COSY experiments show good sensitivity and excellent solvent suppression. The 2D version can be acquired in as little as 45 minutes and the 3D versions acquired overnight. The experiments are demonstrated on a 13C-labeled sample of the second PDZ domain from human phosphatase PTP1E in H2O solution.
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Affiliation(s)
- K Gehring
- McIntyre Medical Science Building, McGill University, 3655 Drummond Street, Montreal, Quebec, H3G 1Y6, Canada.
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13
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Ekiel I, Banville D, Shen SH, Slon-Usakiewicz JJ, Koshy A, Gehring K. Main-chain signal assignment for the PDZ2 domain from human protein tyrosine phosphatase hPTP1E and its complex with a C-terminal peptide from the Fas receptor. J Biomol NMR 1998; 12:455-456. [PMID: 9835052 DOI: 10.1023/a:1008267807859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- I Ekiel
- Sector of Pharmaceutical Biotechnology, National Research Council of Canada, Montréal, PQ, Canada.
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14
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Beglova N, LeSauteur L, Ekiel I, Saragovi HU, Gehring K. Solution structure and internal motion of a bioactive peptide derived from nerve growth factor. J Biol Chem 1998; 273:23652-8. [PMID: 9726969 DOI: 10.1074/jbc.273.37.23652] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conformation and internal dynamics of a bioactive cyclic peptide, N-acetyl-YCTDEKQCY, derived from the C-D loop of beta-nerve growth factor (beta-NGF) were analyzed by solution NMR spectroscopy. NMR experimental data were used to calculate an ensemble of peptide structures. All of the structures had a beta-turn at residues Asp4-Gln7 but could be divided into two families according the presence or absence of a hydrogen bond at Gln7. Comparison of the calculated structures with the corresponding C-D loops from the x-ray structures of the NGF revealed striking similarity. The orientation of Glu5, Lys6, and Gln7 side chains in the NGF mimetic was very similar to the C-D loop of NGF. These residues are known to participate in interactions with the TrkA receptor. Relaxation measurements of the peptidomimetic alpha-carbons at 13C natural abundance and calculated dynamic parameters suggest that the loop region of peptide is well structured but that residues Thr3, Asp4, Glu5, and Lys6 undergo slow conformational exchange. These results suggest that conformational similarity and possibly peptide dynamics are responsible for the bioactivity of the peptide.
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Affiliation(s)
- N Beglova
- Department of Biochemistry and Montreal Joint Centre for Structural Biology, McGill University, 3655 Drummond St., Montréal, Québec H3G 1Y6, Canada
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Hall A, Ekiel I, Mason RW, Kasprzykowski F, Grubb A, Abrahamson M. Structural basis for different inhibitory specificities of human cystatins C and D. Biochemistry 1998; 37:4071-9. [PMID: 9521728 DOI: 10.1021/bi971197j] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human cystatins C and D share almost identical primary structures of two out of the three segments proposed to be of importance for enzyme interactions but have markedly different profiles for inhibition of the target cysteine peptidases, cathepsins B, H, L, and S. To investigate if the N-terminal binding regions of the inhibitors are responsible for the different inhibition profiles, and thereby confer biological selectivity, two hybrid cystatins were produced in Escherichia coli expression systems. In one hybrid, the N-terminal segment of cystatin C was placed on the framework of cystatin D, and the second was engineered with the N-terminal segment of cystatin D on the cystatin C scaffold. Truncated cystatin C and D variants, devoid of their N-terminal segments, were obtained by incubation with glycyl endopeptidase and isolated, in a second approach to assess the importance of the N-terminal binding regions for cystatin function and specificity. The affinities of the four cystatin variants for cathepsins B, H, L, and S were measured. By comparison with corresponding results for wild-type cystatins C and D, it was concluded (1) that both the N-terminal and framework part of the molecules significantly contribute to the observed differences in inhibitory activities of cystatins C and D and (2) that the N-terminal segment of cystatin C increases the inhibitory activity of cystatin D against cathepsin S and cathepsin L but results in decreased activity against cathepsin H. These differences in specificity were explained by the residues interacting with the S2 subsite of peptidases (Val- and Ala-10 in cystatin C and D, respectively). Also, removal of the N-terminal segment results in total loss of enzyme affinity for cystatin D but not for cystatin C. Therefore, structural differences in the framework parts, as well as in the N-terminal segments, are critical for both inhibitory specificity and potency. Homology modeling was used to identify residues likely responsible for the generally reduced inhibitory potency of cystatin D.
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Affiliation(s)
- A Hall
- Department of Clinical Chemistry, Institute of Laboratory Medicine, University of Lund, University Hospital, Sweden
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Berti PJ, Ekiel I, Lindahl P, Abrahamson M, Storer AC. Affinity purification and elimination of methionine oxidation in recombinant human cystatin C. Protein Expr Purif 1997; 11:111-8. [PMID: 9325146 DOI: 10.1006/prep.1997.0763] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recombinant human cystatin C (cC), a cysteine protease inhibitor, contained methionine sulfoxide [Met(O)] residues when expressed in Escherichia coli under aerobic conditions or upon allowing osmotic shock solutions from anaerobically grown cultures to warm to room temperature. Oxidation occurred in the periplasmic space or intracellularly during aerobic expression. Both Met14 and Met41 were subject to oxidation, as determined by NMR spectroscopy and mass spectrometry. Oxidation of Met110 was not observed. Growth under anaerobic conditions and modified purification procedures prevented oxidation. Through the use of a new form of affinity purification, cC was purified to > 99% in one step on E-64-papain-Sepharose (E-64 is 1-[N-[(L-3-trans-carboxyoxirane-2-carbonyl)-L-leucyl]amino]-4-g uanidinobutane), with elution with sodium trichloroacetate. The dissociation equilibrium constants (Kd) for the interaction of unoxidized cC, (Met(O)14)cC, and (Met(O)41)cC with S-(N-ethylsuccinimidyl)papain were experimentally identical: 1.8 (+/-0.2) x 10(-7), 1.6 (+/-0.2) x 10(-7), and 1.4 (+/-0.5) x 10(-7) M, respectively. This implies that the structure of the protease-binding region of mono-oxidized cC's was unchanged. The NMR observation of small, localized conformational changes was consistent with this. (Met(O)14)cC and (Met(O)14,Met(O)41)cC eluted earlier upon analytical affinity chromatography.
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Affiliation(s)
- P J Berti
- Pharmaceutical Biotechnology Sector, Biotechnology Research Institute, National Research Council of Canada, Montréal, Quebec, Canada
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Ekiel I, Abrahamson M, Fulton DB, Lindahl P, Storer AC, Levadoux W, Lafrance M, Labelle S, Pomerleau Y, Groleau D, LeSauteur L, Gehring K. NMR structural studies of human cystatin C dimers and monomers. J Mol Biol 1997; 271:266-77. [PMID: 9268658 DOI: 10.1006/jmbi.1997.1150] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Human cystatin C undergoes dimerization before unfolding. Dimerization leads to a complete loss of its activity as a cysteine proteinase inhibitor. A similar process of dimerization has been observed in cells, and may be related to the amyloid formation seen for the L68Q variant of the protein. Dimerization is barrier controlled, and no dimer/monomer interconversion can be observed at physiological conditions. As a consequence, very stable, "trapped" dimers can be easily separated from monomers. A study of the structural aspects of cystatin C dimer formation was undertaken using NMR spectroscopy. The monomer/dimer model was verified by (pulse field gradient NMR) self-diffusion molecular mass measurements. Complete backbone resonance assignments and secondary structure determination were obtained for the monomer using data from triple resonance experiments performed on 13C/15N doubly labeled protein. A marked similarity of the cystatin C secondary structure to that of chicken cystatin was observed. Using uniformly and amino-acid-specific 15N-enriched protein, backbone NH signals were assigned for cystatin C in its dimeric state. Comparison of 1H -15N correlation NMR spectra of the monomer and dimer shows that the three-dimensional structure remains unchanged in the dimer and that only local perturbations occur. These are localized to the amino acid residues comprising the cysteine proteinase binding site. Such a mode of dimerization readily explains the complete loss of the inhibitory activity in the dimer. The NMR results also demonstrate that the dimer is symmetric.
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Affiliation(s)
- I Ekiel
- Pharmaceutical Biotechnology, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Ave, Montréal, Québec, H4P 2R2, Canada
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Abstract
A major glycolipid was isolated from the well characterized Saccharopolyspora species, S. hirsuta, S. rectivirgula, S. erythraea and one not completely identified strain (Saccharopolyspora sp.). On the basis of sugar and methylation analysis, specific enzymatic and chemical degradations of the carbohydrate moiety, its FAB mass spectrometry and NMR spectroscopy characterizations, the carbohydrate part was shown to be the glycerol linked dimannoside alpha-D-Manp-(1-->3)-alpha-D-Manp-(1-->1/3)Gro. The internal mannose residue is esterified at C-6 by one fatty acid residue, whereas another fatty acyl chain substitutes the primary methylene position of glycerol. The main fatty acyl residues are anteiso-branched heptadecanoic acid and the iso-branched fatty acids iso-17:0, iso-16:0, and iso-18:0, with the former species being predominant. The major glycolipid has potential value for taxonomic and diagnostic purposes, especially in the specific diagnosis of farmer's lung disease.
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Affiliation(s)
- A Gamian
- Polish Academy of Sciences, Institute of Immunology and Experimental Therapy, Wroclaw, Poland
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19
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Abstract
With the aim to improve our understanding of the structural basis for protein self-association and aggregation, in particular in relationship to protein refolding and amyloid formation, folding-related processes for human cystatin C have been studied. Using NMR spectroscopy together with chromatographic and electrophoretic methods, a self-association process resulting in dimer formation for protein samples treated with denaturing agents as well as for samples subjected to low pH or high temperature conditions could be studied with amino acid resolution. In all three cases, the dimerization involves properly folded molecules and proceeds via the reactive site of the inhibitor, which leads to complete loss of its biological activity. This dimerization process has potential relevance for amyloid formation by the brain hemorrhage-causing Leu58-Gln variant of cystatin C. The results also indicate that cystatin C dimerization and inactivation may occur in acidified compartments in vivo, which could be relevant for the physiological regulation of cysteine proteinase activity.
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Affiliation(s)
- I Ekiel
- Pharmaceutical Biotechnology Sector, National Research Council of Canada, Montreal, Quebec, Canada
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Sprott GD, Ferrante G, Ekiel I. Tetraether lipids of Methanospirillum hungatei with head groups consisting of phospho-N,N-dimethylaminopentanetetrol, phospho-N,N,N-trimethylaminopentanetetrol, and carbohydrates. Biochim Biophys Acta 1994; 1214:234-42. [PMID: 7918605 DOI: 10.1016/0005-2760(94)90069-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Acyclic, standard tetraether and diether lipids each account for about 50% of the total ether lipids found in Methanospirillum hungatei. Sixteen ether lipids were purified and defined according to relative weight percentage and staining reactions on thin-layer plates. Structures were elucidated for six previously uncharacterized tetraether lipids. Four of these lipids had as one head group either alpha-glcp-(1-2)-beta-gal(f)-, or beta-gal(f)-(1-6)-beta-gal(f)-, in glycosidic linkage to the first glycerol of the lipid backbone, and either a N,N-dimethyl-aminopentanetetrol or a N,N,N-trimethylaminopentanetetrol moiety in phosphodiester linkage to the second glycerol of the backbone. A fifth lipid was a tetraether structure novel in having carbohydrate moieties at both head group positions; namely alpha-glcp-(1-2)-gal(f)- and beta-gal(f)-. Two other lipids, a diether and a tetraether, had a single head group consisting of alpha-glcp-(1-2)-beta-gal(f)- modified by O-acetylation of the gal(f) residue at C-6. In addition to the seven new lipids described above, diether and tetraether analogs of phosphatidylglycerol were found.
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Affiliation(s)
- G D Sprott
- National Research Council of Canada, Institute for Biological Sciences, Ottawa, Ontario, Canada
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21
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Patel GB, Sprott D, Ekiel I. Production of Specifically Labeled Compounds by
Methanobacterium espanolae
Grown on H
2
-CO
2
plus [
13
C]Acetate. Appl Environ Microbiol 1993; 59:1099-103. [PMID: 16348910 PMCID: PMC202244 DOI: 10.1128/aem.59.4.1099-1103.1993] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanobacterium espanolae
, an acidiphilic methanogen, required acetate for maximal growth on H
2
-CO
2
. In the presence of 5 to 15 mM acetate, at a growth pH of 5.5, the μ
max
was 0.05 h
-1
.
M. espanolae
consumed 12.3 mM acetate during 96 h of incubation at 35°C with shaking at 100 rpm. At initial acetate levels of 2.5 to 10.0 mM, the amount of biomass produced was dependent on the amount of acetate in the medium.
13
C nuclear magnetic resonance spectra of protein hydrolysates obtained from cultures grown on [1-
13
C]- or [2-
13
C]acetate indicated that an incomplete tricarboxylic acid pathway, operating in the reductive direction, was functional in this methanogen. The amino acids were labeled with a very high degree of specificity and at greater than 90% enrichment levels. Less than 2% label randomization occurred between positions primarily labeled from either the carboxyl or methyl group of acetate, and very little label was transferred to positions primarily labeled from CO
2
. The labeling pattern of carbohydrates was typical for glucogenesis from pyruvate. This methanogen, by virtue of the properties described above and its ability to incorporate all of the available acetate (10 mM or lower) from the growth medium, has advantages over other microorganisms for use in the production of specifically labeled compounds.
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Affiliation(s)
- G B Patel
- Institute for Biological Sciences, National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario, Canada K1A 0R6
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22
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Sprott GD, Dicaire CJ, Choquet CG, Patel GB, Ekiel I. Hydroxydiether Lipid Structures in
Methanosarcina
spp. and
Methanococcus voltae. Appl Environ Microbiol 1993; 59:912-4. [PMID: 16348899 PMCID: PMC202207 DOI: 10.1128/aem.59.3.912-914.1993] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydroxylated diether lipids are the most abundant lipids in
Methanosarcina acetivorans, Methanosarcina thermophila
, and
Methanosarcina barkeri
MS and Fusaro, regardless of the substrate used for growth. Structural analysis of the lipid moiety freed of polar head groups revealed that the hydroxydiether lipids of all the
Methanosarcina
strains were hydroxylated at position 3 of
sn
-2 phytanyl chains. The finding that
Methanosarcina
strains synthesize the same hydroxydiether structure suggests that this is a taxonomic characteristic of the genus.
Methanococcus voltae
produced minor amounts of the 3-hydroxydiether characteristic of
Methanosarcina
spp. and also the 3′-hydroxydiether described previously for
Methanosaeta concilii
.
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Affiliation(s)
- G D Sprott
- Institute for Biological Sciences, 100 Sussex Drive, Ottawa, Ontario K1A OR6, Canada
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23
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Sprott GD, Ekiel I, Dicaire C. Novel, acid-labile, hydroxydiether lipid cores in methanogenic bacteria. J Biol Chem 1990; 265:13735-40. [PMID: 2380184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Polar ether lipids extracted from 15 methanogenic bacteria, representative of seven genera, were screened by nuclear magnetic resonance and thin layer chromatography for the presence of hydroxyl groups on the C20-phytanyl moieties. Major amounts of hydroxydiether core lipid were confirmed for Methanosaeta concilii and discovered in two Methanosarcina species, Methanococcus voltae, and tentatively in several Methanobacterium species. Signals at 1.24 and 1.8-1.9 ppm in 1H NMR spectra are characteristic of Methanosaeta concilii lipids hydroxylated on carbon-3 (sn-3 chain). Related signals, which were shifted slightly, appeared in spectra of the polar lipids extracted from both Methanosarcina species. Following mild hydrolysis to remove the polar head groups, only two chromatographically distinct core lipids were found in significant amounts in Methanosarcina barkeri (and Methanosarcina mazei) consisting of 43% 2,3-di-O-phytanyl-sn-glycerol (C20,20-diether) and 57% C20,20-hydroxydiether. This latter core lipid differed from the hydroxydiether from M. concilii by hydroxylation, on carbon-3, of the phytanyl chain in ether linkage to the sn-2 carbon of glycerol. The structural assignment was based on identification of the novel hydroxydiether core and its methylation products by 1H NMR, 13C NMR, and mass spectroscopy. The hydroxy core lipid degraded to various products during standard methanolic HCl and sulfuric acid procedures, including a methoxy derivative (methanolic HCl) and the 3-mono-O-phytanyl-sn-glycerol.
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Affiliation(s)
- G D Sprott
- Division of Biological Sciences, National Research Council of Canada, Ottawa, Ontario
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24
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25
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Affiliation(s)
- D V Awang
- Bureau of Drug Research, Health and Welfare Canada, Ottawa, Ontario
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26
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Ferrante G, Brisson JR, Patel GB, Ekiel I, Sprott GD. Structures of minor ether lipids isolated from the aceticlastic methanogen, Methanothrix concilii GP6. J Lipid Res 1989; 30:1601-9. [PMID: 2614262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Structures were determined for two phospholipids and three glycolipids purified from chloroform-methanol extracts of Methanothrix concilii GP6. Together they accounted for 14% of the total lipid and were based on a C20,20-diether core structure consisting of either 2,3-di-O-phytanyl-sn-glycerol or its 3'-hydroxy analog, namely, 2-O-[3,7,11,15-tetramethylhexadecyl]-3-O-[3'- hydroxy-3',7',11',15'-tetramethylhexadecyl]-sn-glycerol. These two core lipids formed phosphodiester bonds to ethanolamine and glycosidic bonds to beta-D-galactopyranose. A third glycolipid consisted of the triglycosyl head group beta-D-galactopyranosyl-(1----6)-[beta-D-glucopyranosyl-(1----3)]-beta-D - galactopyranose in glycosidic linkage to the 3'-hydroxydiether core lipid.
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Affiliation(s)
- G Ferrante
- Division of Biological Sciences, National Research Council of Canada, Ottawa, Ontario
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27
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Ferrante G, Brisson JR, Patel GB, Ekiel I, Sprott GD. Structures of minor ether lipids isolated from the aceticlastic methanogen, Methanothrix concilii GP6. J Lipid Res 1989. [DOI: 10.1016/s0022-2275(20)38243-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Darzynkiewicz E, Stepinski J, Ekiel I, Goyer C, Sonenberg N, Temeriusz A, Jin Y, Sijuwade T, Haber D, Tahara SM. Inhibition of eukaryotic translation by nucleoside 5'-monophosphate analogues of mRNA 5'-cap: changes in N7 substituent affect analogue activity. Biochemistry 1989; 28:4771-8. [PMID: 2548592 DOI: 10.1021/bi00437a038] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleotide cap analogues of 7-methylguanosine 5'-monophosphate (m7GMP) were synthesized in which the 7-methyl moiety was replaced with 7-ethyl (e7), 7-propyl (p7), 7-isopropyl (ip7), 7-butyl (b7), 7-isobutyl (ib7), 7-cyclopentyl (cp7), 7-(carboxymethyl) (cm7), 7-benzyl (bn7), 7-(2-phenylethyl) [7-(2-PhEt)], and 7-(1-phenylethyl) [7-(1-PhEt)]. These derivatives were assayed as competitive inhibitors of capped mRNA translation in reticulocyte lysate. We observed that N7 alkyl and alicyclic substituents larger than ethyl significantly decreased the inhibitory activity of these cap analogues presumably by decreasing their affinity for cap binding proteins, which participate in the initiation of translation. This result defined a maximum size for this class of N7 substituents in the nucleotide binding domain of cap binding proteins. Like m7GMP, the N7-substituted GMP derivatives synthesized in this study were found to be predominantly in the anti conformation as determined by proton NMR analyses. However, bn7GMP and 7-(2-PhEt)GMP, which have aromatic N7 substituents, were more effective than m7GMP as competitive inhibitors of translation. The increased affinity of bn7GMP for cap binding proteins was further examined by synthesis of beta-globin mRNA containing 5'-bn7G, 5'-m7G, or 5'-e7G cap structures. These modified mRNAs were tested as translation templates. Messenger RNA capped with bn7G was observed to increase the translation activity of the template 1.8-fold relative to that of its m7G-capped mRNA counterpart. By contrast, e7G-capped mRNA was 25% less active than m7G-capped mRNA.2+V photo-cross-linking of m7G-capped mRNA to cap binding proteins
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Affiliation(s)
- E Darzynkiewicz
- Department of Microbiology, University of Southern California School of Medicine, Los Angeles 90033-1054
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29
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Darzynkiewicz E, Stepinski J, Ekiel I, Jin Y, Haber D, Sijuwade T, Tahara SM. Beta-globin mRNAs capped with m7G, m2.7(2)G or m2.2.7(3)G differ in intrinsic translation efficiency. Nucleic Acids Res 1988; 16:8953-62. [PMID: 3174438 PMCID: PMC338645 DOI: 10.1093/nar/16.18.8953] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We examined the intramolecular effect of altered cap structures on translation efficiency of artificial beta-globin mRNAs. For these studies, synthetic dinucleotides of the form X(5')ppp(5')G [X = 7-methyl guanosine (m7G), 2,7-dimethyl guanosine (m2(2,7)G) or 2,2,7-trimethyl guanosine (m3(2,2,7)G)], were transcriptionally incorporated into mRNAs, containing rabbit beta-globin coding sequences, using T7 RNA polymerase and a beta-globin cDNA template. These synthetic mRNAs were assayed in reticulocyte lysate for activity relative to m7G-capped mRNA. m2(2,7)G-Capped mRNA was found to be 1.5-fold more active than m7G-capped mRNA. Messenger RNA capped with m3(2,2,7)G was less active with activity of 0.24 relative to its m7G-capped counterpart (activity = 1.0). These data suggest that m7G-capped mRNAs become more active as translation templates after addition of a single N2 methyl moiety, which is especially pertinent to gene expression in togaviridae. The latter are observed to synthesize m2(2,7)G and m3(2,2,7)G-capped mRNAs in addition to m7G-capped templates during the course of infection in animal cells.
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Affiliation(s)
- E Darzynkiewicz
- Department of Microbiology, USC School of Medicine, Los Angeles 90033-1054
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30
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Abstract
The structure of Citrobacter O23-specific polysaccharide has been shown by sugar and methylation analyses of the native and chemically degraded polysaccharide and by 1H- and 13C-n.m.r. spectroscopy to consist of the tetrasaccharide repeating-units: ----4)-alpha-D-Man-(1----2)-alpha-D-Man-(1----2)-beta-D-Man- (1----3)-alpha-D-GalNAc-(1----, 80% of which are substituted by O-acetyl groups.
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31
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Darzynkiewicz E, Ekiel I, Lassota P, Tahara SM. Inhibition of eukaryotic translation by analogues of messenger RNA 5'-cap: chemical and biological consequences of 5'-phosphate modifications of 7-methylguanosine 5'-monophosphate. Biochemistry 1987; 26:4372-80. [PMID: 2822090 DOI: 10.1021/bi00388a028] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
New analogues of 7-methylguanosine 5'-monophosphate (m7GMP) were synthesized with modified 5'-phosphate moieties by replacement of -O with -H, -CH3, or -NH2. Additional analogues were synthesized with 8-methyl- or 8-aminoguanine base substitutions or ring-opened ribose (2',3'-diol). These compounds were analyzed by 1H and 31P NMR for solution conformation. In addition, they were also analyzed for biological activity as analogues of mRNA 5'-caps by competition as inhibitors of translation in reticulocyte lysate. Substitution of oxygen on the 5'-monophosphate moiety by -H and -CH3 diminished the activity of the cap analogue as a competitive inhibitor; however, replacement by -NH2 did not diminish the activity of the analogue as an inhibitor. It was inferred from this result that cap binding proteins require a hydrogen bond acceptor as opposed to having an exclusive requirement for a second anionic group on the alpha-phosphate moiety. Inhibition results obtained with C8-substituted m7GMP analogues indicated that the 8-amino derivative was a better inhibitor than the 8-methyl derivative of m7GMP. The former is primarily anti whereas the latter is primarily syn with respect to glycosidic bond conformation. This result further supports the model that the anti conformation is the preferred form of the cap structure for interaction with cap binding proteins. The 2',3'-diol derivative of m7GMP was inactive as an inhibitor of translation.
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Affiliation(s)
- E Darzynkiewicz
- Department of Microbiology, University of Southern California School of Medicine, Los Angeles 90033-1054
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32
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Gupta SV, Tourigny G, Stuart AL, De Clercq E, Quail JW, Ekiel I, el-Kabbani OA, Delbaere LT. Relationship between structure and antiviral activity of 5-methoxymethyl-2'-deoxyuridine and 5-methoxymethyl-1-(2'-deoxy-beta-D-lyxofuranosyl)uracil. Antiviral Res 1987; 7:69-77. [PMID: 3034147 DOI: 10.1016/0166-3542(87)90022-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
5-Methoxymethyl-1-(2'-deoxy-beta-D-lyxofuranosyl)uracil (MMdLU) was not active against the herpes simplex viruses. The relationship between molecular conformation and antiviral activity for the two epimers, 5-methoxymethyl-2'-deoxyuridine (MMdUrd) and MMdLU, is discussed. MMdUrd was phosphorylated by the virus-induced deoxythymidine kinase. In contrast, MMdLU did not serve as a substrate for the kinase. The geometry and distance between the 5'-CH2OH and 3'-OH groups of the furanose ring appear to be key factors in determining the efficiency of phosphorylation by the virus-induced deoxythymidine kinase, and hence antiviral activity.
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33
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Ferrante G, Ekiel I, Sprott GD. Structural characterization of the lipids of Methanococcus voltae, including a novel N-acetylglucosamine 1-phosphate diether. J Biol Chem 1986; 261:17062-6. [PMID: 3782154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The lipids of a moderately halophilic methanogen, Methanococcus voltae, accounted for 5.1% of the cell dry weight and consisted of 91% polar lipids and 9% neutral lipids. Twelve polar lipids were detected, three of which, all derivatives of 2,3-di-O-phytanyl-sn-glycerol, were identified as: 2,3-di-O-phytanyl-1-O-[beta-D-glucopyranosyl-(1-6)-beta-D- glucopyranosyl]-sn-glycerol, 2,3-di-O-phytanyl-1-O-[beta-D-glucopyranosyl]-sn-glycerol and a novel NAc-glucosamine 1-phosphate diether, and 2,3-di-O-phytanyl-1-[phosphoryl-2-acetamido-2-deoxy-beta-D- glucopyranosyl]-sn-glycerol. The neutral lipids consisted mainly of squalenes: squalene, dihydrosqualene, tetrahydrosqualene, hexahydrosqualene, and unidentified squalenes.
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34
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Ferrante G, Ekiel I, Sprott GD. Structural characterization of the lipids of Methanococcus voltae, including a novel N-acetylglucosamine 1-phosphate diether. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)75999-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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35
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Ekiel I, Sprott GD, Smith IC. Mevalonic acid is partially synthesized from amino acids in Halobacterium cutirubrum: a 13C nuclear magnetic resonance study. J Bacteriol 1986; 166:559-64. [PMID: 3700337 PMCID: PMC214641 DOI: 10.1128/jb.166.2.559-564.1986] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
13C nuclear magnetic resonance revealed an unusual pathway for the biosynthesis of lipids in Halobacterium cutirubrum and H. halobium. Mevalonic acid was not synthesized from three acetyl-coenzyme A molecules, as has been suggested previously, and the branch-methyl and methine carbons in phytanyl chains were derived from neither acetate nor glycerol. Instead, they were supplied by the degradation of amino acids, in particular of lysine. Presumably, two different types of two-carbon fragments were used simultaneously by halobacteria for the biosynthesis of mevalonate. The labeling pattern of squalene supported the above conclusions. Based on these data, a general scheme is proposed to account for the contribution of lysine-to-lipid biosynthesis.
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36
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Ekiel I, Jarrell KF, Sprott GD. Amino acid biosynthesis and sodium-dependent transport in Methanococcus voltae, as revealed by 13C NMR. Eur J Biochem 1985; 149:437-44. [PMID: 3996416 DOI: 10.1111/j.1432-1033.1985.tb08944.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Of several methanogenic bacteria examined only Methanococcus voltae readily incorporated exogenous amino acids into cell protein. This was easily shown, since growth in the presence of exogenous amino acids resulted in a loss of signal intensities from those carbon atoms normally labelled by [13C]acetate during biosynthesis. From 80% to 95% of the Ser, Lys, Pro or Val incorporated into protein could be supplied directly from the growth medium. In contrast, Asp and Glu, if supplied to the medium, accounted for only a small percentage of the total acidic amino acid used in protein synthesis. Constitutive transport systems took up a wide range of amino acids at rates of 0.1-4.1 nmol min-1 mg-1. The transport systems required Na+, with the possible exception of the basic amino acid lysine, and were inhibited by N-ethylmaleimide or 3,3',4',5-tetrachlorosalicylanilide. No interconversion of Ile to other amino acids was detected when cells were given [13C]Ile during growth, whereas the expected labelling of the Asp and Glu families of amino acids resulted when [13C]Asp was provided to the culture. Mc. voltae synthesized its amino acids from acetate via routes fully consistent with those found in Methanospirillum hungatei [Ekiel, I., Smith, I.C.P. & Sprott, G.D. (1983) J. Bacteriol. 156, 316-326]. Propionate could substitute for an auxotrophic requirement for Ile, resulting in the synthesis of Ile with the beta-carbon originating from the carboxyl of acetate and the alpha-carbon from the carboxyl of propionate. No labelling of Ile from [13C]acetate could occur without the fatty acid. These results provide strong evidence for the carboxylation of propionate to form 2-oxobutyrate as intermediate in Ile biosynthesis, and show that the metabolic defect in Ile biosynthesis occurs prior to 2-oxobutyrate synthesis. The presence of constitutive amino acid transport systems and multiple routes for ile biosynthesis make Methanococcus voltae an attractive methanogen for genetic studies.
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37
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Abstract
Biosynthetic pathways in Methanothrix concilii, a recently isolated aceticlastic methanogen, were studied by 13C-nuclear magnetic resonance spectroscopy. Labeling patterns of amino acids, lipids, and carbohydrates were determined. Similar to other methanogens, acetate was carboxylated to pyruvate, which was further converted to amino acids by various biosynthetic pathways. The origin of carbon atoms in glutamate, proline, and arginine clearly showed that an incomplete tricarboxylic acid cycle operating in the oxidative direction was used for their biosynthesis. Isoleucine was synthesized via citramalate, which is a typical route for methanogens. As with Methanosarcina barkeri, an extensive exchange of the label between the carboxyl group of acetate and CO2 was observed. Lipids predominantly contained diphytanyl chains, the labeling of which indicated that biosynthesis proceeded through mevalonic acid. Labeling of the C-1,6 of glucose from [2-13C]acetate is consistent with a glucogenic route for carbohydrate biosynthesis. Except for the different origins of the methyl group of methionine, the metabolic properties of Methanothrix concilii are closely related to those of Methanosarcina barkeri.
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38
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Abstract
The main metabolic pathways in Methanospirillum hungatei GP1 were followed by using 13C nuclear magnetic resonance, with 13C-labeled acetate and CO2 as carbon sources. The labeling patterns found in carbohydrates, amino acids, lipids, and nucleosides were consistent with the formation of pyruvate from acetate and CO2 as the first step in biosynthesis. Carbohydrates are formed by the glucogenic pathway, and no scrambling of label was observed, indicating that the oxidative or reductive pentose phosphate pathways are not functioning at significant rates. The pathways for amino acid biosynthesis are the usual ones, with the exception of that for isoleucine. The tricarboxylic acid pathway is incomplete and operates in a reductive direction to form alpha-ketoglutarate. The phytanyl chains of lipids are synthesized from acetate via mevalonic acid.
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39
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Deslauriers R, Ekiel I, Kroft T, Smith IC. NMR studies of malaria. 31P nuclear magnetic resonance of blood from mice infected with Plasmodium berghei. Biochim Biophys Acta 1982; 721:449-57. [PMID: 6760901 DOI: 10.1016/0167-4889(82)90101-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
High resolution 31P-NMR has been used for the non-invasive observation of metabolites and metabolic rates in blood of normal mice and of mice infected with Plasmodium berghei, the causative agent of malaria. 31P-NMR was used to quantitate levels of 2,3-diphosphoglycerate in whole cells as a function of the degree of parasitemia and yielded good agreement with the results of enzymatic assays. The time-dependence of 31P metabolites was monitored in both normal and infected erythrocytes, greater rates of decay of 2,3-diphosphoglycerate being observed in malarial blood which correlate with the level of parasitemia. Very high metabolic rates of infected cells render measurement of intracellular pH unreliable on freshly drawn whole blood. When appropriate measures are taken to avoid this complication, no difference is observed in the intracellular pH of parasitized and non-parasitized erythrocytes from infected animals. In both normal and parasitized mice the intraerythrocytic pH is more acidic than that of the suspending medium by 0.15 pH unit at 25 degrees C. Unlike free-living protozoa, the parasitic protozoan Plasmodium does not contain detectable levels of phosphonates or polyphosphates, in either whole cells or perchloric acid extracts thereof.
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40
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Deslauriers R, Ekiel I, Byrd RA, Jarrell HC, Smith IC. A 31P-NMR study of structural and functional aspects of phosphate and phosphonate distribution in Tetrahymena. Biochim Biophys Acta 1982; 720:329-37. [PMID: 7115775 DOI: 10.1016/0167-4889(82)90109-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
31P-NMR has been used to study the chemical nature of cytoplasmic components of live Tetrahymena in a non-invasive manner. The technique has further been used to characterized the physical behaviour of lipids extracted from this organism. In particular, we have shown the presence of large quantities of pyrophosphate and of tripolyphosphate in acid extracts of the organism. These are not detectable in the live cells due to the motionally rigid nature of the storage granules. We have characterized the distribution of phosphonic acids in the organism and followed the phase behavior of the extracted cell lipids. Aqueous dispersions of extracted lipid show both bilayer and non-bilayer behaviour in the range of the growth temperature. The phosphonolipid in Tetrahymena appears to play a role similar to that of phosphatidylethanolamine in regulating the phase behaviour of the membrane. The high degree of unsaturation in the fatty acids of Tetrahymena is most likely responsible for the polymorphic phase behaviour observed near the growth temperature.
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41
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Jarrell HC, Butler KW, Byrd RA, Deslauriers R, Ekiel I, Smith IC. A 2H-NMR study of Acholeplasma laidlawii membranes highly enriched in myristic acid. Biochim Biophys Acta 1982; 688:622-36. [PMID: 7104342 DOI: 10.1016/0005-2736(82)90373-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Myristic acid specifically deuterated at several positions along the acyl chain was biosynthetically incorporated into the membrane lipids of Acholeplasma laidlawii B to the level of greater than or equal to 90%. 2H-NMR was used to study the molecular order and lipid phase composition of the membranes as a function of temperature. Isolated membranes and intact cells give rise to similar 2H spectra. Below 25 degrees C the spectra exhibit a broad gel phase component which at 0 degrees C reaches the rigid limit value expected for an immobilized methylene group. Spectral moments were used to determine the relative amounts of gel and liquid crystalline phase lipids throughout the gel-liquid crystal phase transition. The results indicate that at the growth temperature (37 or 30 degrees C) the A. laidlawii B membrane lipids are approximately 85-90% in the gel state, and that protein has little effect on lipid order of the liquid crystalline lipid, but leads to an increase in the linewidth by approx. 20%.
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Darzynkiewicz E, Antosiewicz J, Ekiel I, Morgan MA, Tahara SM, Shatkin AJ. Methyl esterification of m7G5'p reversibly blocks its activity as an analog of eukaryotic mRNA 5'-caps. J Mol Biol 1981; 153:451-8. [PMID: 7338917 DOI: 10.1016/0022-2836(81)90289-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Birnbaum GI, Cygler M, Ekiel I, Shugar D. Crystal structure and conformation of 8-bromo-9-β- D-xylofuranosyladenine hydrate. Acta Crystallogr A 1981. [DOI: 10.1107/s0108767381097705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ekiel I, Marsh D, Smallbone BW, Kates M, Smith IC. The state of the lipids in the purple membrane of Halobacterium cutirubrum as seen by 31P NMR. Biochem Biophys Res Commun 1981; 100:105-10. [PMID: 7259737 DOI: 10.1016/s0006-291x(81)80069-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Ekiel I, Remin M, Darzynkiewicz E, Shugar D. Correlations of conformational parameters and equilibrium conformational states in a variety of beta-D-arabinonucleosides and their analogues. Biochim Biophys Acta 1979; 562:177-91. [PMID: 444524 DOI: 10.1016/0005-2787(79)90164-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
H nuclear magnetic resonance spectroscopy has been applied to a study of the conformations of a variety of purine and pyrimidine beta-D-arabinofuranosyl nucleosides. The experimental results, together with data collected from the literature, demonstrated the existence of reasonably good correlations between the coupling constants made it possible to define more accurately, than hitherto possible, the conformational states between which equilibria exist in solution. The equilibrium for the arabinonucleosides differs from that previously established for ribonucleosides; in particular, structural modifications and solvent effects may appreciably modify the conformational states between which equilibria exist. Preliminary measurements on some arabinosides in the syn conformation about the glycosidic bond indicated that these do not conform to the foregoing correlations, and will require separate study. A correlation has also been established between the conformation of the arabinose ring and that of the exocyclic 5'-CH2OH group. For both purine and pyrimidine arabinonucleosides, the conformational state 3E of the arabinose ring coexists to some extent with a gauche-gauche conformation of the exocyclic 5'-CH2OH, as in the case of pyrimidine (but not purine) ribonucleosides. Application of the foregoing to some biological problems is described.
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Ekiel I, Darzynkiewicz E, Dudycz L, Shugar D. Solution conformation and relative acidities of the sugar hydroxyls of the O'-methylated derivates of the antimetabolite 9-beta-D-xylofuranosyladenine. Biochemistry 1978; 17:1530-6. [PMID: 25667 DOI: 10.1021/bi00601a027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Remin M, Darzynkiewicz E, Ekiel I, Shugar D. Conformation in aqueous medium of the neutral, protonated and anionic forms of 9-beta-D-arabinofuranosyladenine. Biochim Biophys Acta 1976; 435:405-16. [PMID: 8099 DOI: 10.1016/0005-2787(76)90205-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proton magnetic resonance spectroscopy was employed to study the solution conformations of the neutral, protonated and dissociated forms of the therapeutically active 9-beta-D-arabinofuranosyladenine (araA). In particular, in strongly basic medium, increasing alkalinity led to pronounced changes in chemical shifts and coupling constants of some pentose protons, due to ionization of the pentose hydroxyls, especially the 2'-OH. The neutral form of araA may be characterized as approx. 25% C(2')endo and approx. 60% gauche-gauche, hence somewhat different from that of the therapeutically active 1-beta-D-arabinofuranosylcytosine (araC). By contrast, the conformations of the anionic forms of both of these are identical, predominantly (greater than 80%) C(2')endo and gauche-gauche. With the aid of the 3'-O-methyl derivatives of araA and araC, where only the 2'-OH ionizes, and the accompanying conformational changes are similar, it follows that the conformation C(2')endo and gauche-gauche for all the foregoing is constrained to this form via a strong intramolecular hydrogen bond, viz. O(5')H...O(2')(-). The influence of the foregoing hydrogen bond on the chemical shifts of the adenine H(8) in the araA anion points to the existence of the latter in the form anti. A similar effect of the doubly ionized phosphate group on H(8) in 5'-araAMP shows the nucleotide to also prefer the form anti, as previously demonstrated for 5'-AMP. The conformations of the sugar rings of the neutral forms of araA and adenosine in aqueous medium differ appreciably, whereas in the solid state they are very similar. PMR spectroscopy is shown to be an effective method for following sugar hydroxyl dissociation. The extent of ionization of a given hydroxyl is provided by the resulting chemical shifts of neighbouring (geminal and vicinal) protons. When ionization is accompanied by a change in conformation, the process may be followed also by changes in proton-proton vicinal coupling constants.
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Bogdanowicz E, Ekiel I, Pasiud-Waniek J. [Effect of tricyclic antidepressants on ECG recordings in patients with endogenous depression. Preliminary communication]. Psychiatr Pol 1975; 9:283-8. [PMID: 1153560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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